How to Install PyMOL for Free: Open-Source and Educational License Options (2026)

Open-source vs educational license — which to get

PyMOL is maintained by Schrödinger Inc., which sells commercial licenses. But two free routes exist for academic researchers, and both are legitimate for publication work.

For the vast majority of structural biology work — loading PDB files, coloring structures, making publication figures, visualizing MD trajectories — the open-source version is fully sufficient. Get the educational license only if you specifically need the APBS electrostatics plugin or the additional commercial ray-trace modes.

Method 1 — conda (recommended, all platforms)

Installing via conda works identically on macOS, Windows, and Linux and is the most reliable route regardless of platform. If you don’t have conda installed, download and install Miniconda first from docs.conda.io/en/latest/miniconda.html — the minimal conda distribution takes about two minutes to install.

# Step 1: Create a dedicated PyMOL environment
# (keeps PyMOL's dependencies separate from your other work)
conda create -n pymol python=3.10 -y

# Step 2: Activate the environment
conda activate pymol

# Step 3: Install PyMOL from conda-forge
conda install -c conda-forge pymol-open-source -y

# Step 4: Launch PyMOL
pymol

Method 2 — Homebrew on macOS

# Install Homebrew first if needed (homebrew.sh)
# Then install PyMOL:
brew install pymol

# Launch
pymol

Method 3 — Windows installer

# Install the wheel file directly (replace filename with your version)
pip install pymol_open_source-3.1.0-cp310-cp310-win_amd64.whl

# Launch
pymol

Method 4 — Schrödinger educational license

Verifying the installation

Once installed, run through these checks to confirm PyMOL is working correctly before trying to open your own structures.

# Fetch a test structure from the PDB (requires internet)
fetch 1ubq

# If successful, ubiquitin appears in the viewer
# Then run a basic coloring command:
util.cbc
zoom

# Check your PyMOL version
print(cmd.get_version())

Common installation problems

PyMOL opens but the viewer window is black or blank. This is usually a graphics driver issue. On Linux, try running pymol -M to disable hardware acceleration. On macOS, ensure your system is running the latest GPU drivers. On Windows, update your graphics card drivers from the manufacturer’s website.

“command not found: pymol” after conda install. The conda environment isn’t activated. Run conda activate pymol first. If the error persists after activation, the installation may have failed silently — try conda install -c conda-forge pymol-open-source -y again and watch for error messages.

Apple Silicon Mac: PyMOL crashes on launch. The most reliable fix is to ensure you’re using a conda environment created with CONDA_SUBDIR=osx-arm64 conda create -n pymol before installing. This forces the arm64 architecture throughout the environment.

Educational license key not accepted. The license file must be placed in the correct directory — PyMOL will tell you where it expects it. On macOS this is typically ~/Library/Preferences/PyMOL; on Windows, the AppData folder. If the key was emailed as an attached file rather than a string, save the file directly to that directory rather than copying the text.

Windows: import errors on launch. PyMOL on Windows occasionally has DLL dependency issues if multiple Python installations are present. Use the conda route and ensure you launch PyMOL exclusively from Anaconda Prompt with the pymol environment active — not from a standard Command Prompt or PowerShell.